SARS-CoV-2 Variant Browser

The SARS-CoV-2 Variant Browser is a web based application to explore and visualize SARS-CoV-2 variants, apply spatial, temporal and molecular filters, and view data statistics in an easy-to-use graphical interface.

Prerequiste

• Node.js is required to prepare data and launch application server.
• Python3 is required to prepare data.

Getting Started

First, clone project, install dependencies and build application with the following commands:

git clone https://github.com/IBM/SARS-CoV-2-Variant-Browser
cd SARS-CoV-2-Variant-Browser
npm install
npm run build

Prepare Data

Before exploring variant data with application, data preparation is necessary.

We introduce two properties version and dataset to manage data version and data set in folder and file names. Please follow the naming conventions to create foloder and files in each steps.

1. Obtain or create raw data

   You can obtain sample raw data files from here. Put raw data files in the following structures:

   <data folder(default is ./data)>
   |-- <version>
       |-- <dataset>
           |-- clade_<version>_<dataset>.tsv
           |-- cluster_<version>_<dataset>.tsv
           |-- samples_<version>_<dataset>.tsv
           |-- variant_<version>_<dataset>.tsv
       |-- locations_<version>.csv
   

2. Create stat data from raw data

   Run the following command to generate stat files. Please note that the script requires numpy and pandas.

   python ./tools/StatViewTableProcess/Stat_View_Table_Process.py <version> <dataset>

   Stat data will be generated in the following structures:

   <data folder(default is ./data)>
   |-- <version>
       |-- Stat-<dataset>
         |-- 00_basic_infomation_<version>_<dataset>.csv
         |-- 00_gene_variant_<version>_<dataset>.csv
         |-- ...
         |-- 07_country_clade_week_<version>_<dataset>.csv
   

3. Create JSON data files from raw and stat data:

   Modify DATA_VERSION and DATA_SET environment variables in .env file to specify version and dataset, and run the following command to generate JSON data.

   npm run update-data variant

   Or you can specify environment variables directly in the command line:

   DATA_VERSION=r42 DATA_SET=NCBI npm run update-data variant

   JSON data to be used in the application will be generated in ./data/json folder.

Run Application

Start server with the following command:

npm start

Open http://localhost:3000 with your browser to see the result.

Note that modify DEFAULT_DATA_SET environment variables in .env file to specify dataset.

Run Application in Development Mode

You can run the development server if you need to modify code for your own enhancement:

npm run dev

License

The SARS-CoV-2 Variant Browser is licensed under the Apache Software License, Version 2. The license's full text can be found in LICENSE.